Yes, I ran two test simulations , one with 5 cpu and another with 1; 5 cpu simulation : step 50380, will finish at Wed Nov 21 01:46:25 2012 step 50020, will finish at Wed Nov 21 01:48:36 2012 step 50320, will finish at Wed Nov 21 01:46:49 2012 step 50270, will finish at Wed Nov 21 01:47:07 2012 *Time command :* *real 153m1.968s* *user 0m0.472s* *sys 0m2.072s* * * 1 cpu simulation :(started almost 5 minutes later) step 56000, will finish at Wed Nov 21 02:02:07 2012 *Time command :* *real 177m25.541s* *user 177m23.041s* *sys 0m0.352s* * *
On Tue, Nov 20, 2012 at 8:06 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/20/12 8:43 AM, Parisa Rahmani wrote: > >> Thanks for your reply. >> I have also tried installing with _mpi suffix >> Here is the output of ldd: >> >> gromacs3.3/bin$ ldd mdrun_mpi >> linux-vdso.so.1 => (0x00007fff4658c000) >> libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.**so.1 (0x00007f7d7afe9000) >> libfftw3f.so.3 => /usr/lib/libfftw3f.so.3 (0x00007f7d7ac76000) >> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.**6 (0x00007f7d7a9f3000) >> libmpich.so.3 => /usr/lib/libmpich.so.3 (0x00007f7d7a603000) >> libopa.so.1 => /usr/lib/libopa.so.1 (0x00007f7d7a402000) >> libmpl.so.1 => /usr/lib/libmpl.so.1 (0x00007f7d7a1fd000) >> librt.so.1 => /lib/x86_64-linux-gnu/librt.**so.1 (0x00007f7d79ff5000) >> libcr.so.0 => /usr/lib/libcr.so.0 (0x00007f7d79deb000) >> libpthread.so.0 => /lib/x86_64-linux-gnu/**libpthread.so.0 >> (0x00007f7d79bce000) >> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.**6 (0x00007f7d79847000) >> /lib64/ld-linux-x86-64.so.2 (0x00007f7d7b216000) >> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.**so.2 (0x00007f7d79642000) >> >> ------------------------------**------------------------------** >> ------------------------------**-------------------------- >> gromacs3.3/bin$ ldd mdrun_mpi | grep mpi >> libmpich.so.3 => /usr/lib/libmpich.so.3 (0x00007fc78fb5c000) >> It seems that gromacs has been compiled with mpich. >> >> > Does this executable still give the error listed below? Performance is > one thing, errors are another. You may not necessarily obtain great > scaling, depending on the contents of the system. > > -Justin > > >> >> On Tue, Nov 20, 2012 at 4:15 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 11/19/12 12:09 PM, Parisa Rahmani wrote: >>> >>> Dear gmx users >>>> >>>> I have a problem with running parallel jobs on my Debian system(Openmpi >>>> installed on it), >>>> **Linux debian 3.2.0-1-amd64 #1 SMP , UTC 2012 x86_64 GNU/Linux** >>>> I am using gmx 3.3.3, because of the *lambda dynamics* method which is >>>> >>>> implemented in it. >>>> >>>> AS I know ,in gmx 3.x, the number of processors supplied for the >>>> subsequent >>>> mdrun needed to match the input file. but when i use **grompp -np 6 & >>>> mpirun -np 6 mdrun** the following error appears : >>>> >>>> ERROR : run input file md.tpr was made for 6 nodes, >>>> while mdrun expected it to be for 1 nodes. >>>> >>>> through search of mailing list i found similar problems, but non of >>>> the solutions worked for my case. >>>> >>>> wihtout -np option in grompp the error disappears, and then with each >>>> of these commands >>>> >>>> ** >>>> >>>> 1)mpirun -np 6 mdrun -deffnm md >>>> >>>> 2)mpirun -np 6 mdrun -deffnm md -N 6 >>>> >>>> 3)mpirun -np 6 mdrun -np 6 -deffnm md >>>> >>>> 4)mdrun -np 6 -s md -N 6 >>>> >>>> >>>> **it uses 6 processors(each one at nearly 100%), but the simulation >>>> time is the same as for 1 processor. >>>> >>>> I have no problem with parallel jobs on our cluster(gmx 3.3.3 & >>>> openmpi), with following command: >>>> >>>> ** >>>> grompp -np 6 -f ... >>>> mpiexec mdrun ...(number of processors is specified in the bash file) >>>> ** >>>> , >>>> but i can't run it on my 6 core system. >>>> >>>> Also, I have no problem with newer version of gmx (4.5.x), but i >>>> should use this version, and Hope someone can help me. >>>> >>>> >>>> Have you properly compiled an MPI-enabled mdrun? The default >>> executable >>> name should be mdrun_mpi. It should be linked against libmpi, so running >>> ldd on the mdrun executable should tell you. >>> >>> -Justin >>> >>> -- >>> ==============================****========== >>> >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==============================****========== >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>> posting! >>> >>> * Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
